Spotting the enemy within: Targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family

Lineage specific evolution of the VNTR composite retrotransposon central domain and its role in retrotransposition of gibbon LAVA elements

(2015) Iulia Lupan et al.   BMC GENOMICS

ZNF10 inhibits HIV-1 LTR activity through interaction with NF-κB and Sp1 binding motifs

(2015) Hironori Nishitsuji et al.   FEBS LETTERS

The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses

(2015) Gernot Wolf et al.   GENES & DEVELOPMENT

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes

(2015) Patrick L. Collins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retrotransposons shape species-specific embryonic stem cell gene expression

(2015) Luisa Robbez-Masson et al.   Retrovirology

ORIGIN AND PREVALENCE OF HUMAN T-LYMPHOTROPIC VIRUS TYPE 1 (HTLV-1) AND TYPE 2 (HTLV-2) AMONG INDIGENOUS POPULATIONS IN THE AMERICAS

(2015) Arthur Paiva et al.   REVISTA DO INSTITUTO DE MEDICINA TROPICAL DE SAO PAULO

Endogenous viruses: Connecting recent and ancient viral evolution

(2015) Pakorn Aiewsakun et al.   VIROLOGY

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

(2015) Liana Fasching et al.   Cell Reports

PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination

(2015) Christopher L. Baker et al.   PLoS Genetics

hnRNP K Coordinates Transcriptional Silencing by SETDB1 in Embryonic Stem Cells

(2015) Peter J. Thompson et al.   PLoS Genetics

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

(2015) Ruslan Strogantsev et al.   GENOME BIOLOGY

ZNF282 (Zinc finger protein 282), a novel E2F1 co-activator, promotes esophageal squamous cell carcinoma

(2015) So-Young Yeo et al.   Oncotarget

Transposable elements and psychiatric disorders

(2014) Guia Guffanti et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Repetitive elements dynamics in cell identity programming, maintenance and disease

(2014) Beatrice Bodega et al.   CURRENT OPINION IN CELL BIOLOGY

Identification of Ssm1b, a novel modifier of DNA methylation, and its expression during mouse embryogenesis

(2014) S. Ratnam et al.   DEVELOPMENT

Prdm9 Polymorphism Unveils Mouse Evolutionary Tracks

(2014) H. Kono et al.   DNA RESEARCH

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

Deep Vertebrate Roots for Mammalian Zinc Finger Transcription Factor Subfamilies

(2014) Hui Liu et al.   Genome Biology and Evolution

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

(2014) Priscilla Turelli et al.   GENOME RESEARCH

Endogenous Retroviruses and the Development of Cancer

(2014) G. Kassiotis   JOURNAL OF IMMUNOLOGY

HIV-1 Interacts with Human Endogenous Retrovirus K (HML-2) Envelopes Derived from Human Primary Lymphocytes

(2014) D. Brinzevich et al.   JOURNAL OF VIROLOGY

Regulation of the Human Endogenous Retrovirus K (HML-2) Transcriptome by the HIV-1 Tat Protein

(2014) M. J. Gonzalez-Hernandez et al.   JOURNAL OF VIROLOGY

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

The enemy within: endogenous retroelements and autoimmune disease

(2014) Hannah E Volkman et al.   NATURE IMMUNOLOGY

An improved predictive recognition model for Cys2-His2 zinc finger proteins

(2014) Ankit Gupta et al.   NUCLEIC ACIDS RESEARCH

Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential

(2014) M. Ohnuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trans-activation, post-transcriptional maturation, and induction of antibodies to HERV-K (HML-2) envelope transmembrane protein in HIV-1 infection

(2014) Henri-Alexandre Michaud et al.   Retrovirology

Primate evolution of the recombination regulator PRDM9

(2014) Jerrod J. Schwartz et al.   Nature Communications

The Functional Significance of Common Polymorphisms in Zinc Finger Transcription Factors

(2014) S. H. Lockwood et al.   G3-Genes Genomes Genetics

Kruppel-associated box (KRAB) proteins in the adaptive immune system

(2014) Francesca R Santoni de Sio   Nucleus

The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses

(2013) S Lukic et al.   CELL DEATH AND DIFFERENTIATION

KRAB-Zinc Finger Proteins: A Repressor Family Displaying Multiple Biological Functions

(2013) Angelo Lupo et al.   CURRENT GENOMICS

De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET

(2013) H. M. Rowe et al.   DEVELOPMENT

Epigenetic marking and repression of porcine endogenous retroviruses

(2013) G. Wolf et al.   JOURNAL OF GENERAL VIROLOGY

The Role of Transposable Elements in Health and Diseases of the Central Nervous System

(2013) M. T. Reilly et al.   JOURNAL OF NEUROSCIENCE

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential L1 regulation in pluripotent stem cells of humans and apes

(2013) Maria C. N. Marchetto et al.   NATURE

Endogenous retroviruses function as species-specific enhancer elements in the placenta

(2013) Edward B Chuong et al.   NATURE GENETICS

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation

(2013) C. Lavialle et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global and Stage Specific Patterns of Krüppel-Associated-Box Zinc Finger Protein Gene Expression in Murine Early Embryonic Cells

(2013) Andrea Corsinotti et al.   PLoS One

Endogenous retrovirus-K promoter: a landing strip for inflammatory transcription factors?

(2013) Mamneet Manghera et al.   Retrovirology

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

(2013) I. Barde et al.   SCIENCE

Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells

(2013) Xiaoying Tan et al.   Stem Cell Research

A common mode of recognition for methylated CpG

(2013) Yiwei Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

Recognizing the enemy within: licensing RNA-guided genome defense

(2013) Phillip A. Dumesic et al.   TRENDS IN BIOCHEMICAL SCIENCES

Transposable elements as genetic regulatory substrates in early development

(2013) Wesley D. Gifford et al.   TRENDS IN CELL BIOLOGY

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

DNA binding specificities of the long zinc-finger recombination protein PRDM9

(2013) Timothy Billings et al.   GENOME BIOLOGY

Association of Endogenous Retroviruses and Long Terminal Repeats with Human Disorders

(2013) Iyoko Katoh et al.   Frontiers in Oncology

Gene knockout and knockin by zinc-finger nucleases: current status and perspectives

(2012) J. Hauschild-Quintern et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

ZBRK1 represses HIV-1 LTR-mediated transcription

(2012) Hironori Nishitsuji et al.   FEBS LETTERS

Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons

(2012) Lucia Carbone et al.   Genome Biology and Evolution

TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells

(2012) H. M. Rowe et al.   GENOME RESEARCH

Liver-specific ablation of Krüppel-associated box-associated protein 1 in mice leads to male-predominant hepatosteatosis and development of liver adenoma

(2012) Karolina Bojkowska et al.   HEPATOLOGY

Whole exome sequencing identified a novel zinc-finger geneZNF141associated with autosomal recessive postaxial polydactyly type A

(2012) Umm-e- Kalsoom et al.   JOURNAL OF MEDICAL GENETICS

The KRAB Zinc Finger Protein RSL1 Regulates Sex- and Tissue-Specific Promoter Methylation and Dynamic Hormone-Responsive Chromatin Configuration

(2012) C. J. Krebs et al.   MOLECULAR AND CELLULAR BIOLOGY

RNAi triggered by specialized machinery silences developmental genes and retrotransposons

(2012) Soichiro Yamanaka et al.   NATURE

Endogenous viruses: insights into viral evolution and impact on host biology

(2012) Cédric Feschotte et al.   NATURE REVIEWS GENETICS

SUMOylation of ZFP282 potentiates its positive effect on estrogen signaling in breast tumorigenesis

(2012) E J Yu et al.   ONCOGENE

Targeted Disruption in Mice of a Neural Stem Cell-Maintaining, KRAB-Zn Finger-Encoding Gene That Has Rapidly Evolved in the Human Lineage

(2012) Huan-Chieh Chien et al.   PLoS One

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

The clf2 gene has an epigenetic role in the multifactorial etiology of cleft lip and palate in the A/WySn mouse strain

(2011) Jenna A. Plamondon et al.   BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY

Retrotransposition and genomic imprinting

(2011) M. Cowley et al.   Briefings in Functional Genomics

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

The TRIM Family Protein KAP1 Inhibits HIV-1 Integration

(2011) Awatef Allouch et al.   Cell Host & Microbe

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

Coevolution of retroelements and tandem zinc finger genes

(2011) J. H. Thomas et al.   GENOME RESEARCH

Endogenous APOBEC3B Restricts LINE-1 Retrotransposition in Transformed Cells and Human Embryonic Stem Cells

(2011) Silke Wissing et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gypsy and the Birth of the SCAN Domain

(2011) R. O. Emerson et al.   JOURNAL OF VIROLOGY

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements

(2011) Serena De Fazio et al.   NATURE

Relationship between Gene Body DNA Methylation and Intragenic H3K9me3 and H3K36me3 Chromatin Marks

(2011) Maria A. Hahn et al.   PLoS One

Endogenous retrovirus drives hitherto unknown proapoptotic p63 isoforms in the male germ line of humans and great apes

(2011) Ulrike Beyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Silencing of endogenous retroviruses: when and why do histone marks predominate?

(2011) Danny C. Leung et al.   TRENDS IN BIOCHEMICAL SCIENCES

Cell-to-cell transmission of retroviruses: Innate immunity and interferon-induced restriction factors

(2011) Clare Jolly   VIROLOGY

Dynamic control of endogenous retroviruses during development

(2011) Helen M. Rowe et al.   VIROLOGY

HTLV-3/STLV-3 and HTLV-4 Viruses: Discovery, Epidemiology, Serology and Molecular Aspects

(2011) Renaud Mahieux et al.   Viruses-Basel

The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans

(2011) Laure Ségurel et al.   PLOS BIOLOGY

Small RNA-Mediated Quiescence of Transposable Elements in Animals

(2010) Kuniaki Saito et al.   DEVELOPMENTAL CELL

A LINE-1 component to human aging: Do LINE elements exact a longevity cost for evolutionary advantage?

(2010) Georges St. Laurent et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Rapid Sequence and Expression Divergence Suggest Selection for Novel Function in Primate-Specific KRAB-ZNF Genes

(2010) K. Nowick et al.   MOLECULAR BIOLOGY AND EVOLUTION

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans

(2010) Ingrid L Berg et al.   NATURE GENETICS

Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma

(2010) Björn Lamprecht et al.   NATURE MEDICINE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

ZNF274 Recruits the Histone Methyltransferase SETDB1 to the 3′ Ends of ZNF Genes

(2010) Seth Frietze et al.   PLoS One

Prdm9 Controls Activation of Mammalian Recombination Hotspots

(2010) E. D. Parvanov et al.   SCIENCE

Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination

(2010) S. Myers et al.   SCIENCE

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

(2010) F. Baudat et al.   SCIENCE

Island Biogeography Reveals the Deep History of SIV

(2010) M. Worobey et al.   SCIENCE

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

(2010) Anna C. Groner et al.   PLoS Genetics

ZBRK1 Acts as a Metastatic Suppressor by Directly Regulating MMP9 in Cervical Cancer

(2009) L.-F. Lin et al.   CANCER RESEARCH

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

(2009) Carla J. Cohen et al.   GENE

The effect of OTK18 upregulation in U937 cells on neuronal survival

(2009) Christine E. Gilling et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL

Genomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263

(2009) Seth Frietze et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of Episomal Gene Expression by KRAB/KAP1-Mediated Histone Modifications

(2009) I. Barde et al.   JOURNAL OF VIROLOGY

Regulation of the Transcription Factor YY1 in Mitosis through Phosphorylation of Its DNA-binding Domain

(2009) Raed Rizkallah et al.   MOLECULAR BIOLOGY OF THE CELL

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

Origin and evolution of the adaptive immune system: genetic events and selective pressures

(2009) Martin F. Flajnik et al.   NATURE REVIEWS GENETICS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Extraordinary Molecular Evolution in the PRDM9 Fertility Gene

(2009) James H. Thomas et al.   PLoS One

Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain

(2009) Katja Nowick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

(2009) Peter L. Oliver et al.   PLoS Genetics

Adaptive Evolution in Zinc Finger Transcription Factors

(2009) Ryan O. Emerson et al.   PLoS Genetics

Host Restriction Factors Blocking Retroviral Replication

(2008) Daniel Wolf et al.   Annual Review of Genetics

Retroviral promoters in the human genome

(2008) Andrew B. Conley et al.   BIOINFORMATICS

The Protein-Binding Potential of C2H2 Zinc Finger Domains

(2008) Kathryn J. Brayer et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Keep Your Fingers Off My DNA: Protein–Protein Interactions Mediated by C2H2 Zinc Finger Domains

(2008) Kathryn J. Brayer et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

A Maternal-Zygotic Effect Gene, Zfp57, Maintains Both Maternal and Paternal Imprints

(2008) Xiajun Li et al.   DEVELOPMENTAL CELL

OTK18 Levels in Plasma and Cerebrospinal Fluid Correlate with Viral Load and CD8 T-cells in Normal and AIDS Patients

(2008) James L. Buescher et al.   Journal of Neuroimmune Pharmacology

Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57

(2008) Deborah J G Mackay et al.   NATURE GENETICS

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution

(2008) R. J. Gifford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Mapping of Crossovers Reveals Extensive Variation in Fine-Scale Recombination Patterns Among Humans

(2008) G. Coop et al.   SCIENCE

A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase

(2008) O. Mihola et al.   SCIENCE